Well, this applies more to the GIT than the ARE, but basically it's unpredictable and the unintended side effects can break your game. For example, if you place a GIT in Override, everything about the module will be reset every time it is loaded - whether you are loading a save or transitioning from another module. This means any doors you opened will be closed again, anyone you killed will be alive again, anyone who was spawned after the module was loaded will no longer be there, and so on. So that's why you shouldn't do it. I do it, but only for testing purposes and because I'm a very bad boy. I haven't really had reason to do it much with the ARE so I'm not sure if it can be as dangerous, but the files are similar in nature. Anyway, you could probably get away with it, just be careful.